Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags

TLDR

Sediment in aquatic environments harbors high microbial diversity, yet freshwater and intertidal communities have been understudied compared to marine sediments. The study employed millions of Illumina reads from Pearl River sediments to compare bacterial communities across freshwater, intertidal wetland, and marine environments with a consistent sequencing approach. Taxon richness and evenness were highest in freshwater, intermediate in intertidal, and lowest in marine sediments; PCA separated communities at phylum and OTU levels, and LEfSe identified distinct taxa enriched in each sediment type, highlighting freshwater dominance of Acidobacteria, Nitrospira, Verrucomicrobia, Alphaproteobacteria, Betaproteobacteria, intertidal enrichment of Chloroflexi, Bacillariophyta, Gammaproteobacteria, Epsilonproteobacteria, Actinomycetales, Bacteroidetes, Firmicutes, and marine enrichment of Gammaproteobacteria and Deltaproteobacteria involved in sulfate reduction.

Abstract

Sediment, a special realm in aquatic environments, has high microbial diversity. While there are numerous reports about the microbial community in marine sediment, freshwater and intertidal sediment communities have been overlooked. The present study determined millions of Illumina reads for a comparison of bacterial communities in freshwater, intertidal wetland, and marine sediments along Pearl River, China, using a technically consistent approach. Our results show that both taxon richness and evenness were the highest in freshwater sediment, medium in intertidal sediment, and lowest in marine sediment. The high number of sequences allowed the determination of a wide variety of bacterial lineages in all sediments for reliable statistical analyses. Principal component analysis showed that the three types of communities could be well separated from phylum to operational taxonomy unit (OTU) levels, and the OTUs from abundant to rare showed satisfactory resolutions. Statistical analysis (LEfSe) demonstrated that the freshwater sediment was enriched with Acidobacteria, Nitrospira, Verrucomicrobia, Alphaproteobacteria, and Betaproteobacteria. The intertidal sediment had a unique community with diverse primary producers (such as Chloroflexi, Bacillariophyta, Gammaproteobacteria, and Epsilonproteobacteria) as well as saprophytic microbes (such as Actinomycetales, Bacteroidetes, and Firmicutes). The marine sediment had a higher abundance of Gammaproteobacteria and Deltaproteobacteria, which were mainly involved in sulfate reduction in anaerobic conditions. These results are helpful for a systematic understanding of bacterial communities in natural sediment environments.